This chapter deals with RNA viruses that infect vertebrates, and highlights how differences between the biology of DNA and RNA viruses and differences among RNA viruses may help to determine how they can be detected by their hosts. Genetic material restricts the way in which RNA viruses can be maintained within infected individuals. The chapter briefly describes general concepts of viral replication that depend on the nature of the RNA genome. Much effort has recently been focused on further characterizing the nature of the nucleic acid ligands and how they are produced in the viral life cycle. Pattern recognition receptors (PRRs) and their ligands and how they relate to the life cycle of different RNA virus families are briefly reviewed in the chapter. Viruses that establish a chronic infection will need to combat a sustained offense provided by the host’s antiviral immune response. The chapter also reviews two remarkably different RNA virus pathogens, foot-and-mouth disease virus (FMDV) and hepatitis C virus (HCV), to contrast alternate and effective strategies to counteract the innate immune responses of their host.

Replication cycle of viruses with an ssRNA genome of positive polarity. Viral genomic RNA is translated after uncoating to produce the viral proteins. Viral proteins then transcribe the genome into the minus-sense antigenome that, in turn, serves as a template for progeny genome synthesis. Progeny genomes and viral structural proteins assemble into progeny virions.

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Figure 1

Replication cycle of viruses with an ssRNA genome of positive polarity. Viral genomic RNA is translated after uncoating to produce the viral proteins. Viral proteins then transcribe the genome into the minus-sense antigenome that, in turn, serves as a template for progeny genome synthesis. Progeny genomes and viral structural proteins assemble into progeny virions.

Replication cycle of viruses with an ssRNA genome of negative polarity. Viral genomes remain associated with the nucleocapsid protein (N) and are transcribed into mRNAs by the RdRP, which is carried into the host cell by the virion. Viral structural and nonstructural proteins are translated from the mRNAs. Nonstructural proteins serve to replicate the genome into its plus-sense antigenomic complement, which serves as a template for more genome synthesis. Nucleocapsid-associated genomes and viral structural proteins (including the RdRP) then assemble into progeny virions.

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Figure 2

Replication cycle of viruses with an ssRNA genome of negative polarity. Viral genomes remain associated with the nucleocapsid protein (N) and are transcribed into mRNAs by the RdRP, which is carried into the host cell by the virion. Viral structural and nonstructural proteins are translated from the mRNAs. Nonstructural proteins serve to replicate the genome into its plus-sense antigenomic complement, which serves as a template for more genome synthesis. Nucleocapsid-associated genomes and viral structural proteins (including the RdRP) then assemble into progeny virions.

Replication cycle of viruses with an ssRNA genome of ambisense polarity. Nucleocapsid-associated genomes are transcribed into mRNAs for the nucleocapsid protein (N) and the RdRP. N and RdRP are involved in synthesis of the antigenome and progeny genomes. Antigenomes serve as templates for the transcription of mRNAs for structural and other viral proteins. Structural proteins and progeny genomes then assemble into progeny virions.

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Figure 3

Replication cycle of viruses with an ssRNA genome of ambisense polarity. Nucleocapsid-associated genomes are transcribed into mRNAs for the nucleocapsid protein (N) and the RdRP. N and RdRP are involved in synthesis of the antigenome and progeny genomes. Antigenomes serve as templates for the transcription of mRNAs for structural and other viral proteins. Structural proteins and progeny genomes then assemble into progeny virions.

Replication cycle of viruses with dsRNA genomes. dsRNA genomes are transcribed into viral mRNAs within subviral core-particles by the core-associated RdRP. mRNAs are then extruded into the cytoplasm of the host cell and translated into viral proteins. mRNAs and viral proteins assemble into subviral particles, where synthesis of the minus-strand RNA occurs to yield replicated dsRNA. Subviral particles then initiate a secondary round of transcription, translation, packaging, and replication, producing newly formed cores that combine with structural proteins to form progeny virions.

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Figure 4

Replication cycle of viruses with dsRNA genomes. dsRNA genomes are transcribed into viral mRNAs within subviral core-particles by the core-associated RdRP. mRNAs are then extruded into the cytoplasm of the host cell and translated into viral proteins. mRNAs and viral proteins assemble into subviral particles, where synthesis of the minus-strand RNA occurs to yield replicated dsRNA. Subviral particles then initiate a secondary round of transcription, translation, packaging, and replication, producing newly formed cores that combine with structural proteins to form progeny virions.